Dotenv Setup

pangyplot setup is a utility to configure the PangyPlot environment.

This configures the environment by generating a .env file. This file contains key variables that define application parameters.

If a .env file already exists, you will be prompted whether to overwrite it. Existing values are shown as defaults, and you may press Enter to accept them.

Environment Variables

The following variables are supported:

  • GA_TAG_ID (optional) Google Analytics tag ID. Default: None

Cytoband Settings

  • ORGANISM (optional) Organism key used to select the cytoband reference. Must be one of the keys defined in pangyplot/organisms.py: human-hg38, human-t2t, mouse, fruitfly, zebrafish, chicken, rabbit, dog, or the special values custom (bring your own cytoband) or none (no cytoband). Default: human-hg38.

  • CYTOBAND_PATH (conditional) Path to a custom cytoband file. Required only if ORGANISM=custom. Default: none.

  • CANONICAL_PATH (conditional) Path to a canonical chromosome definition file (one chromosome name per line). Required only if ORGANISM=custom. Default: none.

Note

If your organism is not one of the built-ins, pangyplot cytoband generates a dummy cytoband from a reference FASTA index, giving you the two files above. Setting ORGANISM=none runs PangyPlot without a cytoband.

For Production Deployment

  • PANGYPLOT_DATA (optional) Absolute path to the directory containing PangyPlot database files. Default: the datastore/ directory next to wsgi.py.

  • PANGYPLOT_DB (optional) Name of the PangyPlot database. Default: _default_.

  • PANGYPLOT_ANNOTATION (optional) Annotation dataset to load with the graph. Default: None.

  • PANGYPLOT_REF (optional) Reference genome identifier used by the dataset. Default: None.

  • PANGYPLOT_PORT (optional) Port number for running the PangyPlot web application. Default: 5700.